Re: 1-5 Intramolecular repulsions

From: rocwhite168 (rocwhite168_at_163.com)
Date: Wed Nov 05 2014 - 13:02:55 CST

HI Kenno,

In some force fields hydrogen atoms are modeled by a single positive
point charge without LJ potentials. This will create difficulty in
molecules like 1,2-diols, because hydrogen in a OH group will want to
be on top of oxygen in the neighboring OH group. Adding a special 1,5
repulsion term helps solve the problem. Similar issues exist for TIP4P
model, for example, if you run GCMC or GEMC.

Regards,

Roc

On Wed, Nov 5, 2014 at 12:33 PM, Kenno Vanommeslaeghe
<kvanomme_at_rx.umaryland.edu> wrote:
> While the answer is in all likelihood "no", the question is poorly
> formulated; I read it a few times over and I'm still confused about what
> exactly you're looking for (and I work on force fields on a daily basis). Do
> you mean "exceptions" instead of "interactions"? Also, if you want an R^-12
> repulsion without R^-6 attraction (which raises questions about the
> rationale behind the force field), you also have to worry about whether NAMD
> lets you specify them separately (I honestly don't know). Finally, your "for
> example" link doesn't work; it likely relies on form data that is not
> contained in the URL.
>
> On 11/05/2014 12:54 PM, Rebecca Lindsey wrote:
>>
>> Dear All,
>>
>> Is there a way to include 1-5 (intramolecular) interactions in NAMD? As
>> far as I understand, neither NBFIX nor NBTABLE can be used to accomplish
>> this, as do not allow for a distinction between intra- and inter-molecular
>> interactions.
>>
>> The repulsion term in question would be along the lines of: E_repel =
>> a_repel/(r_ij)^12, as it is given by the TraPPE force field. (see, for
>> example: http://www.chem.umn.edu/groups/siepmann/trappe/molname.php)
>>
>> Thanks in advance for your insights.
>>
>> --
>> Rebecca K. Lindsey
>> ----------------------------------------------------
>> Ph. D. Candidate Website <https://sites.google.com/site/rebeccalindseycv/>
>> University of Minnesota LinkedIn
>> <http://www.linkedin.com/pub/rebecca-lindsey/17/b92/10>
>> Twin Cities r.lindsey78_at_gmail.com <mailto:r.lindsey78_at_gmail.com>
>> UMN Chemical Theory Center linds360_at_umn.edu <mailto:linds360_at_umn.edu>
>> ----------------------------------------------------
>
>
>

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